Investigation of proven vaccine breakthrough by SARS-CoV-2 variants in established UK healthcare worker cohorts: SIREN consortium & PITCH Plus Pathway

Lead Research Organisation: Public Health England
Department Name: National Infection Service

Abstract

This project builds on the established PHE SIREN and associated cohorts (PITCH and HICC) working with leading immunologists and scientists to improve understanding of the immune response to infection and vaccines and study in detail those individuals who have proven vaccine breakthrough. These studies are following more than 45,000 healthcare workers, 94% of whom have received two doses of vaccine, and will assess their immune system response to COVID-19 infections and vaccinations.

Understanding the immune response is essential to determine who is most at risk of infections after vaccination, and also for vaccine developers who can target key components of the immune response effectively for future boost vaccines. The adaptive immune system has two major components - B-cells and T-cells. The B-cells produce antibodies that can be detected after previous infection or vaccination. We will be studying two that are expressed against proteins from the virus - the Spike (S) and Nucleocapsid (N) proteins that are measured using assays that can give us the quantity of each present and also a measurement of neutralising or "sterilising" immunity - assessing how well an individual's blood can kill or neutralise either a live SARS-CoV-2 virus or a lab created replica. The T-cells directly kill virus infected cells by releasing proteins known as cytokines, which can signal to other cells and provide instructions to the immune system on its strength and range of response.

The research is focused on key areas:
1. Why do some people get reinfections or infections after vaccination?
2. In individuals who get infections after vaccination, can we identify which parts of their immune system are not working to provide immune protection?
3. How long does this immunity from vaccinations last and how does it differ with different vaccines?
4. How does the immune system respond to booster doses of vaccination?
5. How do changes in the SARS-CoV-2 virus genetic make-up cause evasion of the immune response?
6. What are the differences that can be detected in the human genetic code that are associated with different immune responses to the virus and vaccination?

We will assess these questions using blood from key groups of individuals recruited into our cohort studies to assess the immune response. We will study:
a) individuals who have a re-infection (a second infection after having a previous confirmed infection) and one or two doses of vaccination and
b) individuals who develop an infection after two doses of vaccine.

We can do this effectively because all individuals who are in the study have PCR tests every two weeks and regular blood tests for antibodies that are stored for future analysis. In addition, for individuals who develop infections after vaccination, we will discuss with them in more detail to determine whether they could have a functional problem with their immune system, take specific medications that could prevent their immune system from responding and seek their consent to take additional blood tests to perform detailed analysis of their immune response to COVID. This will involve analysis of their blood tests before and after the infection episode and we will ask if they would like to participate in genetic analysis of their DNA code to see if there are particular mutations in their DNA code that might predict a poor response to vaccination.

We will seek to do this scientifically using specific study designs that will compare individuals who acquire an infection after vaccination to others who do not get infections, matched to age, sex, ethnicity, and co-morbidities. The T and B-cell immune responses will be compared to determine if there are key detectable differences between these groups.

Technical Summary

The SIREN Consortium aims to investigate the correlates of immunity against SARS-CoV-2 post-vaccination, including the durability of the immune response in healthcare workers (HCW).
The study uses the strengths of the largest global cohort study (N~45,000) with regular serological and alternate weekly SARS-CoV-2 PCR testing.
This additional funding enables detailed immunological nested case-control studies where cases are infections post-vaccination and compared to appropriately matched controls. 75 proven vaccine breakthrough cases have already been identified and daily alerts for new infections are in place.

It will assess host and pathogen factors related to infections post-vaccination with the PITCH Plus pathway
1. Anti-S and anti-N neutralising antibodies against the current SARS-CoV-2 variants of concern, using validated pseudovirus microneutralisation (pMN) assay and live virus MN & Tcell memory responses, by IFNG Elispot and T cell proliferation assay
2. The durability of binding and quantification S and N antibody, neutralising antibody and T-cell responses in recipients of different vaccines and vaccination schedules
3. Genotype to phenotype mapping including centralised genomic surveillance for all cases, analysis and exploratory assessment to better define the correlates of humoral and cellular immunity for novel mutations/ emerging variants.
4. Clinical immunology consultation: individuals with post-vaccine infections will be invited to a telephone consultation to review their medical history, have bloods undertaken to assess underlying health conditions, associated immunodeficiency and the humoral and cellular immune system.
5. Human genotyping with consent we will obtain and store genetic material from vaccine breakthrough cases to enable future assessment of known single nucleotide polymorphisms and where necessary whole genome sequencing for associations with suboptimal vaccine response and immunodeficiency.

People

ORCID iD

Susan Hopkins (Principal Investigator) orcid http://orcid.org/0000-0001-5179-5702
Eleanor Barnes (Co-Investigator)
Christopher James Duncan (Co-Investigator) orcid http://orcid.org/0000-0003-4181-2315
Jasmin Islam (Co-Investigator)
Helen Elizabeth Baxendale (Co-Investigator)
Meera Chand (Co-Investigator)
Dan Wootton (Co-Investigator) orcid http://orcid.org/0000-0002-5903-3881
Massimo Palmarini (Co-Investigator)
Victoria Jane Hall (Co-Investigator) orcid http://orcid.org/0000-0001-8744-4277
Paul Klenerman (Co-Investigator)
Brian James Willett (Co-Investigator)
Thushan De Silva (Co-Investigator)
Wendy Barclay (Co-Investigator)
Jonathan Luke Heeney (Co-Investigator)
Amanda Semper (Co-Investigator) orcid http://orcid.org/0000-0003-3656-1363
Lance Turtle (Co-Investigator) orcid http://orcid.org/0000-0002-0778-1693
Timothy John Brooks (Co-Investigator)
Maria Zambon (Co-Investigator)
Rupert Beale (Co-Investigator) orcid http://orcid.org/0000-0002-6705-8560
John Kenneth Baillie (Co-Investigator) orcid http://orcid.org/0000-0001-5258-793X
André Charlett (Co-Investigator)
Alex Gisela Richter (Co-Investigator)
Colin Stewart Brown (Co-Investigator) orcid http://orcid.org/0000-0003-4776-3403
Susanna Jane Dunachie (Co-Investigator) orcid http://orcid.org/0000-0001-5665-6293
Rebecca Payne (Researcher)
Erola Pairo Castineira (Researcher Co-Investigator) orcid http://orcid.org/0000-0002-2423-3090
Edward Carr (Researcher Co-Investigator) orcid http://orcid.org/0000-0001-9343-4593
Iain Milligan (Researcher Co-Investigator) orcid http://orcid.org/0000-0002-6501-5524
Javier Castillo-Olivares (Researcher Co-Investigator) orcid http://orcid.org/0000-0003-3453-8557
Ashley Otter (Researcher Co-Investigator) orcid http://orcid.org/0000-0002-8317-9194
Ana Carolina Atti (Researcher Co-Investigator)
 
Description Member of COVID-19 nMABs and Antivirals Access and Policy National Expert Group (DHSC)
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Likely to be reducing mortality in the most vulnerable groups.
 
Description NICE therapeutics panel
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact Ensured correct advice on neutralising monoclonals wrt variants.
 
Description Presentation of results to Department of Health and Social Care
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
Impact Quantitative information on changes in vaccine-induced antibody and T cell responses with omicron variant compared to delta and Wuhan strain.
 
Description Variant Technical Group
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact The knowledge and risk assessments on emerging variants is used to inform government policy on travel, COVID-19 restrictions, healthcare resources and workforce planning.
URL https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings
 
Description Further articles in London review of Books on COVID-19 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact https://www.lrb.co.uk/the-paper/v43/n24/rupert-beale/on-omicron
Year(s) Of Engagement Activity 2020,2021
URL https://www.lrb.co.uk/the-paper/v43/n24/rupert-beale/on-omicron
 
Description Living with immunodeficiency, living with COVID Webinar. Organised in collaboration with British Socitey of Immunology Immunodeficiency UK UKPIN and the COVAD study 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Webinar in response to national concern from immunodeficiency patients about national policy to remove covid restrictions without a specific plan for this patient group who remain vulnerable due to poor response to vaccination. Collaborating with our key patient organisation, our national professional network UKPIN and the BSI. ~Speakers include patient rep, chair of UKPIN, and co lead in COVAD Professor Burns. We delivered 3 talks around covid through the waves for our patients, vaccine responses and treatment options. There was a 30 minutes Q&A. Questions from this will be taken forward to lobby the government through these partner organisations
Year(s) Of Engagement Activity 2022
URL https://www.immunology.org/events/living-immunodeficiency-living-covid-19
 
Description Oral presentations at European Congress of Clinical Microbiology & Infectious Diseases 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Abstracts have been selected for presentation at ECCMID 2022 in Lisbon, Portugal April 23rd-26th 2022, the 32nd meeting of this large international infectious diseases conference.
Including:
26/04, 13:30 - 15:30 WET 2-Hour Oral Session
12. COVID-19 vaccine immunogenicity, efficacy and effectiveness
1. Ashley Otter "Determinants of SARS-CoV-2 anti-spike antibody levels following BNT162b2 vaccination: a cross-sectional analysis of 6,000 UK healthcare workers (SIREN study)"
2. Victoria Hall "Effectiveness and durability of protection against future SARS-CoV-2 infection conferred by COVID-19 vaccination and previous infection: findings from the UK SIREN prospective cohort study of healthcare workers March 2020 to September 2021"
3. Susanna Dunachie "Humoral and cellular immunity to SARS-CoV-2 from vaccination and infections: the UK PITCH consortium"
Year(s) Of Engagement Activity 2022
URL https://www.eccmid.org/scientific_programme/2022_programme_live_sync/
 
Description PPI (Patient and Public Involvement) Panel 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact A PPI workstream is a key aspect of the SIREN Consortium and something the team are keen to continue after seeing positive impact so far with communications and regular feedback from participants. There have also been participant webinars which facilitated the identification of common questions and issue from participants and the subsequent development of new or additional resources for participants. The PPI panel will provide an in-depth understanding of the participant experience and maximise the potential of SIREN going forwards.

Two PPI Panels have been convened so far, and going forward they are scheduled every six weeks.
Benefits have already been realised in terms of feedback from participants on future research priorities and recruitment and retention strategies.
Year(s) Of Engagement Activity 2022
 
Description Participation in a visit from the Minister for Health Maggie Throup to unit to discuss role of SIREN and Consortium in contributing to Policy 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Minister for Health visited site to discuss the research work that SIREN was delivering in order to deliver on policy objectives related to vaccines
Year(s) Of Engagement Activity 2022
 
Description Presentations at UK Variant Technical Group and Joint Committee of Vaccinations and Immunisations 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The work from SIREN and PItch Plus consortium including the basic science work has been presented to the Variant Technical group and resulting reports and also to JCVI who lead on the recommendations for vaccines to Ministers.
Year(s) Of Engagement Activity 2021,2022
URL https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings
 
Description Visit from shadow health secretary 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Visit from shadow health minister and local MP to hear about the COVID work that had been undertaken in Birmingham. Presented COVAD and highlighted the difficulties for immunodeficiency patients who remain vulnerable to feed into the labour strategy of living with COVID. The Local MP tabled a question in parliament to raise this issue in response to the visit.
Year(s) Of Engagement Activity 2022